Quick Glimpse
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Structure of this guide
This is an example report showing the major parts of microbiome data
analysis workflows.
Mothur Microbiome Snakemake Workflow
We use snakemake [@Dadasnake2021] to
maintain reproducibility and improvement of the bioinformatics analysis
of microbiome data.

Example of common FAQs (in progress)
-
Mothur dist.seqs taking too long.
-
Length of the merged reads (merged reads over 300pb).
-
Not enough overlaping when merging the paired reads.
-
Use other pre-cluster algorithm like Deblur.
-
Too many uniques?
-
Not enough computer power?: Use HPC or Cluster.
-
Try to make contigs using maxee instead of deltaq or use phylogeny
approach for downstream analysis, or use clister.split based on
taxonomy.
-
do not forget to use controls.
References